Leech Heart (HE) Motor Neuron conductances contributions to NN activity (Lamb & Calabrese 2013)

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Accession:153355
"... To explore the relationship between conductances, and in particular how they influence the activity of motor neurons in the well characterized leech heartbeat system, we developed a new multi-compartmental Hodgkin-Huxley style leech heart motor neuron model. To do so, we evolved a population of model instances, which differed in the density of specific conductances, capable of achieving specific output activity targets given an associated input pattern. ... We found that the strengths of many conductances, including those with differing dynamics, had strong partial correlations and that these relationships appeared to be linked by their influence on heart motor neuron activity. Conductances that had positive correlations opposed one another and had the opposite effects on activity metrics when perturbed whereas conductances that had negative correlations could compensate for one another and had similar effects on activity metrics. "
Reference:
1 . Lamb DG, Calabrese RL (2013) Correlated conductance parameters in leech heart motor neurons contribute to motor pattern formation. PLoS One 8:e79267 [PubMed]
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Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Leech;
Cell Type(s): Leech heart motor neuron (HE);
Channel(s): I Na,p; I A; I K; I K,leak; I K,Ca; I Sodium; I Calcium; I Na, leak;
Gap Junctions: Gap junctions;
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: GENESIS;
Model Concept(s): Action Potential Initiation; Activity Patterns; Bursting; Temporal Pattern Generation; Detailed Neuronal Models; Parameter sensitivity; Conductance distributions;
Implementer(s): Lamb, Damon [Damon.Lamb at neurology.ufl.edu];
Search NeuronDB for information about:  I Na,p; I A; I K; I K,leak; I K,Ca; I Sodium; I Calcium; I Na, leak;
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LambCalabrese2013
Scripts
loopsghines.sh
runsghines.sh
                            
#!/bin/bash
# MG version - assumes gang 8 and 12 
# assumes $SGE_TASK_ID, $1 as the generation number (for accessing the .p & .g files) and $2 as ganglion

# To use this file, create a current_generation.par file (either in MOEA or 'manually' - i.e., with matlab) with the names of
# each model instance you wish to simulate.

# to make changes easier to read, defined paths with trailing /:
BASECENTRAL="./"
BASELOCAL="/var/tmp/HE_8_12_sim/"

#----------------------------------------------------
# SGE_TASK_ID=##    # will be passed by qsub when actually used. Override (set) with looping script for serial execution.
#----------------------------------------------------

INPUT="input/" # change before upload to cluster as appropriate
OUTPUT="./"       
GENESIS="lgenesis-noX/"

echo "generation" ${1}

# ensure central directory exists 
if [ ! -d "$BASECENTRAL" ]; then
	echo "central dir does not exist"
	exit
fi
# ensure local directory exists
if [ ! -d "$BASELOCAL" ]; then
    mkdir -p $BASELOCAL
fi

# copy data & files to node if not already present.
# core binaries & scripts: 
# assert the presence of the lgenesis (nxgenesis) core & genesis scripts
cp -r ${BASECENTRAL}"lgenesis-noX_Hines" $BASELOCAL$GENESIS

# evolution and parameter set specific data:
# assert the presence of the input data on the node
cp -r $BASECENTRAL$INPUT $BASELOCAL #$INPUT
# extract current paramset from the current_generation file with sed ${i}'q;d' $FILENAME or awk 'NR=='$i' {print;exit}' $FILENAME
#echo PARAM=`sed ${SGE_TASK_ID}'q;d' ${BASECENTRAL}current_generation.par`
PARAM=`sed ${SGE_TASK_ID}'q;d' ${BASECENTRAL}current_generation.par`
# copy the .p and .g files to the node's local base dir      
cp ${BASECENTRAL}generation_${1}/$PARAM.g $BASELOCAL
cp ${BASECENTRAL}generation_${1}/$PARAM.p $BASELOCAL

# kick off lgenesis with .g file                           OPTIONAL -- do not copy files and run from central dir if using a distributed fs
#-----------------------nx for l -----------------------------------------------------------------------------------------
time ${BASELOCAL}${GENESIS}lgenesis -altsimrc $BASELOCAL$GENESIS.simrc $BASELOCAL$PARAM.g #> /dev/null #>${BASELOCAL}lgencapture.txt

# kick off analysis script         data to be analyzed filename        .fit filename        ganglion number  # of bursts

# copy back soma VM and conductance/current data to central dir
for gang in 8 12 #7 8 9 10 11 12 13 14
do
	mv $BASELOCAL${OUTPUT}HE${gang}soma_Vm${SGE_TASK_ID}.txt ${BASECENTRAL}manipulations/${PARAM}/original/${PARAM}_HE${gang}soma_Vm.txt
	#mv $BASELOCAL${OUTPUT}HE${gang}_AllCurrents.txt ${BASECENTRAL}intermediate_data/${PARAM}_HE${gang}_AllCurrents${SGE_TASK_ID}.txt
	#mv $BASELOCAL${OUTPUT}HE${gang}_AllConductances.txt ${BASECENTRAL}intermediate_data/${PARAM}_HE${gang}_AllConductances${SGE_TASK_ID}.txt
	#mv $BASELOCAL${OUTPUT}HE${gang}_K_Ca_currents${SGE_TASK_ID}.txt ${BASECENTRAL}intermediate_data/${PARAM}_HE${gang}_K_Ca_currents${SGE_TASK_ID}.txt
	#mv $BASELOCAL${OUTPUT}HE${gang}_K_Ca_Header${SGE_TASK_ID}.txt ${BASECENTRAL}intermediate_data/${PARAM}_HE${gang}_K_Ca_Header${SGE_TASK_ID}.txt
	## Alternatively, copy back the output files to rawdata/
	#mv ${BASELOCAL}HE${gang}_AllConductances.txt ${BASECENTRAL}rawdata/${PARAM}_Conductances.txt
	#mv ${BASELOCAL}HE${gang}_AllCurrents.txt ${BASECENTRAL}rawdata/${PARAM}_Currents.txt

	#mv ${BASELOCAL}HE${gang}_AllCondHeader.txt ${BASECENTRAL}rawdata/${PARAM}_CondHeader.txt

done
# cleanup time
# delete lgenesis output files, .p and .g (.p and .g retained on central node)
#rm $BASELOCAL$OUTPUT*.txt
rm $BASELOCAL$PARAM.g $BASELOCAL$PARAM.p

# fin